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Ehrit J, Gräwert TW, Göddeke H, Konarev PV, Svergun DI, Nagel N. Small-angle x-ray scattering investigation of the integration of free fatty acids in polysorbate 20 micelles. Biophys J 2024; 123:S0006-3495(24)00211-X. [PMID: 38547861 PMCID: PMC10995418 DOI: 10.1016/j.bpj.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2024] Open
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Ermakov AV, Chapek SV, Lengert EV, Konarev PV, Volkov VV, Artemov VV, Soldatov MA, Trushina DB. Microfluidically Assisted Synthesis of Calcium Carbonate Submicron Particles with Improved Loading Properties. Micromachines (Basel) 2023; 15:16. [PMID: 38276844 PMCID: PMC10818696 DOI: 10.3390/mi15010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024]
Abstract
The development of advanced methods for the synthesis of nano- and microparticles in the field of biomedicine is of high interest due to a range of reasons. The current synthesis methods may have limitations in terms of efficiency, scalability, and uniformity of the particles. Here, we investigate the synthesis of submicron calcium carbonate using a microfluidic chip with a T-shaped oil supply for droplet-based synthesis to facilitate control over the formation of submicron calcium carbonate particles. The design of the chip allowed for the precise manipulation of reaction parameters, resulting in improved porosity while maintaining an efficient synthesis rate. The pore size distribution within calcium carbonate particles was estimated via small-angle X-ray scattering. This study showed that the high porosity and reduced size of the particles facilitated the higher loading of a model peptide: 16 vs. 9 mass.% for the particles synthesized in a microfluidic device and in bulk, correspondingly. The biosafety of the developed particles in the concentration range of 0.08-0.8 mg per plate was established by the results of the cytotoxicity study using mouse fibroblasts. This innovative approach of microfluidically assisted synthesis provides a promising avenue for future research in the field of particle synthesis and drug delivery systems.
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Affiliation(s)
- Alexey V. Ermakov
- Institute of Molecular Theranostics, First Moscow State Medical University, 119991 Moscow, Russia; (E.V.L.); (D.B.T.)
| | - Sergei V. Chapek
- The Smart Materials Research Institute, Southern Federal University, Sladkova 178/24, 344090 Rostov-on-Don, Russia; (S.V.C.); (M.A.S.)
| | - Ekaterina V. Lengert
- Institute of Molecular Theranostics, First Moscow State Medical University, 119991 Moscow, Russia; (E.V.L.); (D.B.T.)
| | - Petr V. Konarev
- Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, 119333 Moscow, Russia; (P.V.K.); (V.V.V.); (V.V.A.)
| | - Vladimir V. Volkov
- Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, 119333 Moscow, Russia; (P.V.K.); (V.V.V.); (V.V.A.)
| | - Vladimir V. Artemov
- Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, 119333 Moscow, Russia; (P.V.K.); (V.V.V.); (V.V.A.)
| | - Mikhail A. Soldatov
- The Smart Materials Research Institute, Southern Federal University, Sladkova 178/24, 344090 Rostov-on-Don, Russia; (S.V.C.); (M.A.S.)
| | - Daria B. Trushina
- Institute of Molecular Theranostics, First Moscow State Medical University, 119991 Moscow, Russia; (E.V.L.); (D.B.T.)
- Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, 119333 Moscow, Russia; (P.V.K.); (V.V.V.); (V.V.A.)
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Ershova MO, Taldaev A, Konarev PV, Peters GS, Valueva AA, Ivanova IA, Kraevsky SV, Kozlov AF, Ziborov VS, Ivanov YD, Archakov AI, Pleshakova TO. Selection of Aptamers for Use as Molecular Probes in AFM Detection of Proteins. Biomolecules 2023; 13:1776. [PMID: 38136647 PMCID: PMC10742151 DOI: 10.3390/biom13121776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Currently, there is great interest in the development of highly sensitive bioanalytical systems for diagnosing diseases at an early stage, when pathological biomarkers are present in biological fluids at low concentrations and there are no clinical manifestations. A promising direction is the use of molecular detectors-highly sensitive devices that detect signals from single biomacromolecules. A typical detector in this class is the atomic force microscope (AFM). The high sensitivity of an AFM-based bioanalysis system is determined by the size of the sensing element of an atomic force microscope-the cantilever-the radius of the curvature of which is comparable to that of a biomolecule. Biospecific molecular probe-target interactions are used to ensure detection system specificity. Antibodies, aptamers, synthetic antibodies, and peptides can be used as molecular probes. This study has demonstrated the possibility of using aptamers as molecular probes for AFM-based detection of the ovarian cancer biomarker CA125. Antigen detection in a nanomolar solution was carried out using AFM chips with immobilized aptamers, commercially available or synthesized based on sequences from open sources. Both aptamer types can be used for antigen detection, but the availability of sequence information enables additional modeling of the aptamer structure with allowance for modifications necessary for immobilization of the aptamer on an AFM chip surface. Information on the structure and oligomeric composition of aptamers in the solution was acquired by combining small-angle X-ray scattering and molecular modeling. Modeling enabled pre-selection, before the experimental stage, of aptamers for use as surface-immobilized molecular probes.
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Affiliation(s)
- Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Amir Taldaev
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Petr V. Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninsky Ave. 59, 119333 Moscow, Russia
- National Research Centre “Kurchatov Institute”, Akademika Kurchatova Square 1, 123182 Moscow, Russia
| | - Georgy S. Peters
- National Research Centre “Kurchatov Institute”, Akademika Kurchatova Square 1, 123182 Moscow, Russia
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Sergey V. Kraevsky
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Alexander I. Archakov
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Tatyana O. Pleshakova
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
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4
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Ehrit J, Gräwert TW, Göddeke H, Konarev PV, Svergun DI, Nagel N. Small-angle x-ray scattering investigation of the integration of free fatty acids in polysorbate 20 micelles. Biophys J 2023; 122:3078-3088. [PMID: 37340636 PMCID: PMC10432221 DOI: 10.1016/j.bpj.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 06/22/2023] Open
Abstract
A critical quality attribute for liquid formulations is the absence of visible particles. Such particles may form upon polysorbate hydrolysis resulting in release of free fatty acids into solution followed by precipitation. Strategies to avoid this effect are of major interest for the pharmaceutical industry. In this context, we investigated the structural organization of polysorbate micelles alone and upon addition of the fatty acid myristic acid (MA) by small-angle x-ray scattering. Two complementary approaches using a model of polydisperse core-shell ellipsoidal micelles and an ensemble of quasiatomistic micelle structures gave consistent results well describing the experimental data. The small-angle x-ray scattering data reveal polydisperse mixtures of ellipsoidal micelles containing about 22-35 molecules per micelle. The addition of MA at concentrations up to 100 μg/mL reveals only marginal effects on the scattering data. At the same time, addition of high amounts of MA (>500 μg/mL) increases the average sizes of the micelles indicating that MA penetrates into the surfactant micelles. These results together with molecular modeling shed light on the polysorbate contribution to fatty acid solubilization preventing or delaying fatty acid particle formation.
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Affiliation(s)
- Jörg Ehrit
- Analytical Research and Development, NBE Analytical R&D, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen, Germany
| | - Tobias W Gräwert
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Hendrik Göddeke
- Computational Drug Discovery, Small Molecule Therapeutics & Platform Technologies, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen, Germany
| | - Petr V Konarev
- A. V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Сrystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany.
| | - Norbert Nagel
- Analytical Research and Development, Global Technical Centers, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen, Germany.
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Kichkailo AS, Narodov AA, Komarova MA, Zamay TN, Zamay GS, Kolovskaya OS, Erakhtin EE, Glazyrin YE, Veprintsev DV, Moryachkov RV, Zabluda VV, Shchugoreva I, Artyushenko P, Mironov VA, Morozov DI, Khorzhevskii VA, Gorbushin AV, Koshmanova AA, Nikolaeva ED, Grinev IP, Voronkovskii II, Grek DS, Belugin KV, Volzhentsev AA, Badmaev ON, Luzan NA, Lukyanenko KA, Peters G, Lapin IN, Kirichenko AK, Konarev PV, Morozov EV, Mironov GG, Gargaun A, Muharemagic D, Zamay SS, Kochkina EV, Dymova MA, Smolyarova TE, Sokolov AE, Modestov AA, Tokarev NA, Shepelevich NV, Ozerskaya AV, Chanchikova NG, Krat AV, Zukov RA, Bakhtina VI, Shnyakin PG, Shesternya PA, Svetlichnyi VA, Petrova MM, Artyukhov IP, Tomilin FN, Berezovski MV. Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells. Molecular Therapy - Nucleic Acids 2023; 32:267-288. [PMID: 37090419 PMCID: PMC10119962 DOI: 10.1016/j.omtn.2023.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Here, we present DNA aptamers capable of specific binding to glial tumor cells in vitro, ex vivo, and in vivo for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies. These aptamers were used for in situ, ex vivo tissue staining, histopathological analyses, and fluorescence-guided tumor and PET/CT tumor visualization in mice with xenotransplanted human astrocytoma. The aptamers did not show in vivo toxicity in the preclinical animal study. This study demonstrates the potential applications of aptamers for precise diagnostics and fluorescence-guided surgery of brain tumors.
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Affiliation(s)
- Anna S. Kichkailo
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Corresponding author: Anna S. Kichkailo, Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia.
| | - Andrey A. Narodov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Maria A. Komarova
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Tatiana N. Zamay
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Galina S. Zamay
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Olga S. Kolovskaya
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Evgeniy E. Erakhtin
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Yury E. Glazyrin
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Dmitry V. Veprintsev
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Roman V. Moryachkov
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Vladimir V. Zabluda
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Irina Shchugoreva
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Polina Artyushenko
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Vladimir A. Mironov
- Department of Chemistry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, South Korea
| | - Dmitry I. Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland
| | - Vladimir A. Khorzhevskii
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Regional Pathology-Anatomic Bureau, 3d Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Anton V. Gorbushin
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Anastasia A. Koshmanova
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Elena D. Nikolaeva
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Igor P. Grinev
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Ivan I. Voronkovskii
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Daniil S. Grek
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Kirill V. Belugin
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Alexander A. Volzhentsev
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Oleg N. Badmaev
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Natalia A. Luzan
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Kirill A. Lukyanenko
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Georgy Peters
- National Research Center Kurchatov Institute, 1 Akademika Kurchatova, Moscow 123182, Russia
| | - Ivan N. Lapin
- Laboratory of Advanced Materials and Technology, Siberian Physical-Technical Institute of Tomsk State University, 36 Lenina, Tomsk 634050, Russia
| | - Andrey K. Kirichenko
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Petr V. Konarev
- National Research Center Kurchatov Institute, 1 Akademika Kurchatova, Moscow 123182, Russia
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” RAS, 59 Leninsky pr., Moscow 119333, Russia
| | - Evgeny V. Morozov
- Institute of Chemistry and Chemical Technology SB RAS – The Branch of Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, Krasnoyarsk 660036, Russia
| | - Gleb G. Mironov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
| | - Ana Gargaun
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
| | - Darija Muharemagic
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
| | - Sergey S. Zamay
- Department of Molecular Electronics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Elena V. Kochkina
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Maya A. Dymova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 8 Lavrentyev Avenue, Novosibirsk 630090, Russia
| | - Tatiana E. Smolyarova
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Alexey E. Sokolov
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Andrey A. Modestov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Nikolay A. Tokarev
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Nikolay V. Shepelevich
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Anastasia V. Ozerskaya
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Natalia G. Chanchikova
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Alexey V. Krat
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Regional Clinical Cancer Center, 16 1-ya Smolenskaya, Krasnoyarsk 660133, Russia
| | - Ruslan A. Zukov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Regional Clinical Cancer Center, 16 1-ya Smolenskaya, Krasnoyarsk 660133, Russia
| | - Varvara I. Bakhtina
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Pavel G. Shnyakin
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Pavel A. Shesternya
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Valery A. Svetlichnyi
- Laboratory of Advanced Materials and Technology, Siberian Physical-Technical Institute of Tomsk State University, 36 Lenina, Tomsk 634050, Russia
| | - Marina M. Petrova
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Ivan P. Artyukhov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Felix N. Tomilin
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
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6
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Sokolova OS, Pichkur EB, Maslova ES, Kurochkina LP, Semenyuk PI, Konarev PV, Samygina VR, Stanishneva-Konovalova TB. Local Flexibility of a New Single-Ring Chaperonin Encoded by Bacteriophage AR9 Bacillus subtilis. Biomedicines 2022; 10:biomedicines10102347. [PMID: 36289609 PMCID: PMC9598537 DOI: 10.3390/biomedicines10102347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/25/2022] Open
Abstract
Chaperonins, a family of molecular chaperones, assist protein folding in all domains of life. They are classified into two groups: bacterial variants and those present in endosymbiotic organelles of eukaryotes belong to group I, while group II includes chaperonins from the cytosol of archaea and eukaryotes. Recently, chaperonins of a prospective new group were discovered in giant bacteriophages; however, structures have been determined for only two of them. Here, using cryo-EM, we resolved a structure of a new chaperonin encoded by gene 228 of phage AR9 B. subtilis. This structure has similarities and differences with members of both groups, as well as with other known phage chaperonins, which further proves their diversity.
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Affiliation(s)
- Olga S. Sokolova
- Faculty of Biology, MSU-BIT Shenzhen University, Shenzhen 518172, China
| | - Evgeny B. Pichkur
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | | | - Lidia P. Kurochkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Pavel I. Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Petr V. Konarev
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Shubnikov Institute of Crystallography of FSRC “Crystallography and Photonics”, RAS, 119333 Moscow, Russia
| | - Valeriya R. Samygina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Shubnikov Institute of Crystallography of FSRC “Crystallography and Photonics”, RAS, 119333 Moscow, Russia
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7
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Bernardini A, Lorenzo M, Chaves-Sanjuan A, Swuec P, Pigni M, Saad D, Konarev PV, Graewert MA, Valentini E, Svergun DI, Nardini M, Mantovani R, Gnesutta N. The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding. Int J Biol Macromol 2021; 193:401-413. [PMID: 34673109 DOI: 10.1016/j.ijbiomac.2021.10.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 10/20/2022]
Abstract
The trimeric CCAAT-binding NF-Y is a "pioneer" Transcription Factor -TF- known to cooperate with neighboring TFs to regulate gene expression. Genome-wide analyses detected a precise stereo-alignment -10/12 bp- of CCAAT with E-box elements and corresponding colocalization of NF-Y with basic-Helix-Loop-Helix (bHLH) TFs. We dissected here NF-Y interactions with USF1 and MAX. USF1, but not MAX, cooperates in DNA binding with NF-Y. NF-Y and USF1 synergize to activate target promoters. Reconstruction of complexes by structural means shows independent DNA binding of MAX, whereas USF1 has extended contacts with NF-Y, involving the USR, a USF-specific amino acid sequence stretch required for trans-activation. The USR is an intrinsically disordered domain and adopts different conformations based on E-box-CCAAT distances. Deletion of the USR abolishes cooperative DNA binding with NF-Y. Our data indicate that the functionality of certain unstructured domains involves adapting to small variation in stereo-alignments of the multimeric TFs sites.
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Affiliation(s)
- Andrea Bernardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Mariangela Lorenzo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | | | - Paolo Swuec
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Matteo Pigni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Dana Saad
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Petr V Konarev
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Science, Moscow 119333, Russian Federation
| | | | - Erica Valentini
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany
| | - Marco Nardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy.
| | - Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy.
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8
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Konarev PV, Graewert MA, Jeffries CM, Fukuda M, Cheremnykh TA, Volkov VV, Svergun DI. EFAMIX, a tool to decompose inline chromatography SAXS data from partially overlapping components. Protein Sci 2021; 31:269-282. [PMID: 34767272 PMCID: PMC8740826 DOI: 10.1002/pro.4237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/06/2021] [Accepted: 11/09/2021] [Indexed: 11/25/2022]
Abstract
Small‐angle X‐ray scattering (SAXS) is an established technique for structural analysis of biological macromolecules in solution. During the last decade, inline chromatography setups coupling SAXS with size exclusion (SEC‐SAXS) or ion exchange (IEC‐SAXS) have become popular in the community. These setups allow one to separate individual components in the sample and to record SAXS data from isolated fractions, which is extremely important for subsequent data interpretation, analysis, and structural modeling. However, in case of partially overlapping elution peaks, inline chromatography SAXS may still yield scattering profiles from mixtures of components. The deconvolution of these scattering data into the individual fractions is nontrivial and potentially ambiguous. We describe a cross‐platform computer program, EFAMIX, for restoring the scattering and concentration profiles of the components based on the evolving factor analysis (EFA). The efficiency of the program is demonstrated in a number of simulated and experimental SEC‐SAXS data sets. Sensitivity and limitations of the method are explored, and its applicability to IEC‐SAXS data is discussed. EFAMIX requires minimal user intervention and is available to academic users through the program package ATSAS as from release 3.1.
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Affiliation(s)
- Petr V Konarev
- Laboratory of Reflectometry and Small-angle Scattering, A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
| | - Melissa A Graewert
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
| | - Cy M Jeffries
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
| | - Masakazu Fukuda
- Formulation Development Department, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan
| | | | - Vladimir V Volkov
- Laboratory of Reflectometry and Small-angle Scattering, A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
| | - Dmitri I Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
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9
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Kordyukova LV, Konarev PV, Fedorova NV, Shtykova EV, Ksenofontov AL, Loshkarev NA, Dadinova LA, Timofeeva TA, Abramchuk SS, Moiseenko AV, Baratova LA, Svergun DI, Batishchev OV. The Cytoplasmic Tail of Influenza A Virus Hemagglutinin and Membrane Lipid Composition Change the Mode of M1 Protein Association with the Lipid Bilayer. Membranes (Basel) 2021; 11:772. [PMID: 34677538 PMCID: PMC8541430 DOI: 10.3390/membranes11100772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/27/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022]
Abstract
Influenza A virus envelope contains lipid molecules of the host cell and three integral viral proteins: major hemagglutinin, neuraminidase, and minor M2 protein. Membrane-associated M1 matrix protein is thought to interact with the lipid bilayer and cytoplasmic domains of integral viral proteins to form infectious virus progeny. We used small-angle X-ray scattering (SAXS) and complementary techniques to analyze the interactions of different components of the viral envelope with M1 matrix protein. Small unilamellar liposomes composed of various mixtures of synthetic or "native" lipids extracted from Influenza A/Puerto Rico/8/34 (H1N1) virions as well as proteoliposomes built from the viral lipids and anchored peptides of integral viral proteins (mainly, hemagglutinin) were incubated with isolated M1 and measured using SAXS. The results imply that M1 interaction with phosphatidylserine leads to condensation of the lipid in the protein-contacting monolayer, thus resulting in formation of lipid tubules. This effect vanishes in the presence of the liquid-ordered (raft-forming) constituents (sphingomyelin and cholesterol) regardless of their proportion in the lipid bilayer. We also detected a specific role of the hemagglutinin anchoring peptides in ordering of viral lipid membrane into the raft-like one. These peptides stimulate the oligomerization of M1 on the membrane to form a viral scaffold for subsequent budding of the virion from the plasma membrane of the infected cell.
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Affiliation(s)
- Larisa V. Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (L.V.K.); (N.V.F.); (A.L.K.); (L.A.B.)
| | - Petr V. Konarev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, 119333 Moscow, Russia; (P.V.K.); (E.V.S.); (L.A.D.)
| | - Nataliya V. Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (L.V.K.); (N.V.F.); (A.L.K.); (L.A.B.)
| | - Eleonora V. Shtykova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, 119333 Moscow, Russia; (P.V.K.); (E.V.S.); (L.A.D.)
| | - Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (L.V.K.); (N.V.F.); (A.L.K.); (L.A.B.)
| | - Nikita A. Loshkarev
- Laboratory of Bioelectrochemistry, Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Lubov A. Dadinova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, 119333 Moscow, Russia; (P.V.K.); (E.V.S.); (L.A.D.)
| | - Tatyana A. Timofeeva
- Laboratory of Physiology of Viruses, D. I. Ivanovsky Institute of Virology, FSBI N. F. Gamaleya NRCEM, Ministry of Health of Russian Federation, 123098 Moscow, Russia;
| | - Sergei S. Abramchuk
- Department of Chemistry, Lomonosov Moscow State University, 119234 Moscow, Russia;
- Laboratory of Physical Chemistry of Polymers, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Andrei V. Moiseenko
- Laboratory of Electron Microscopy, Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Lyudmila A. Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (L.V.K.); (N.V.F.); (A.L.K.); (L.A.B.)
| | | | - Oleg V. Batishchev
- Laboratory of Bioelectrochemistry, Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119991 Moscow, Russia;
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10
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Manalastas-Cantos K, Konarev PV, Hajizadeh NR, Kikhney AG, Petoukhov MV, Molodenskiy DS, Panjkovich A, Mertens HDT, Gruzinov A, Borges C, Jeffries CM, Svergun DI, Franke D. ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. J Appl Crystallogr 2021; 54:343-355. [PMID: 33833657 PMCID: PMC7941305 DOI: 10.1107/s1600576720013412] [Citation(s) in RCA: 363] [Impact Index Per Article: 121.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/06/2020] [Indexed: 11/11/2022] Open
Abstract
The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus-based concentration-independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi-atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy - a PyMOL plugin to run a subset of ATSAS tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.
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Affiliation(s)
- Karen Manalastas-Cantos
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Petr V. Konarev
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Nelly R. Hajizadeh
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Maxim V. Petoukhov
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Dmitry S. Molodenskiy
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Alejandro Panjkovich
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Andrey Gruzinov
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Clemente Borges
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
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11
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Konarev PV, Gruzinov AY, Mertens HDT, Svergun DI. Restoring structural parameters of lipid mixtures from small-angle X-ray scattering data. J Appl Crystallogr 2021; 54:169-179. [PMID: 33833646 PMCID: PMC7941313 DOI: 10.1107/s1600576720015368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 11/19/2020] [Indexed: 11/26/2022] Open
Abstract
Small-angle X-ray scattering (SAXS) is widely utilized to study soluble macromolecules, including those embedded into lipid carriers and delivery systems such as surfactant micelles, phospho-lipid vesicles and bilayered nanodiscs. To adequately describe the scattering from such systems, one needs to account for both the form factor (overall structure) and long-range-order Bragg reflections emerging from the organization of bilayers, which is a non-trivial task. Presently existing methods separate the analysis of lipid mixtures into distinct procedures using form-factor fitting and the fitting of the Bragg peak regions. This article describes a general approach for the computation and analysis of SAXS data from lipid mixtures over the entire angular range of an experiment. The approach allows one to restore the electron density of a lipid bilayer and simultaneously recover the corresponding size distribution and multilamellar organization of the vesicles. The method is implemented in a computer program, LIPMIX, and its performance is demonstrated on an aqueous solution of layered lipid vesicles undergoing an extrusion process. The approach is expected to be useful for the analysis of various types of lipid-based systems, e.g. for the characterization of interactions between target drug molecules and potential carrier/delivery systems.
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Affiliation(s)
- Petr V. Konarev
- A. V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Andrey Yu. Gruzinov
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg, 22607, Germany
| | - Haydyn D. T. Mertens
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg, 22607, Germany
| | - Dmitri I. Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg, 22607, Germany
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12
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Czech A, Konarev PV, Goebel I, Svergun DI, Wills PR, Ignatova Z. Author Correction: Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes. Sci Rep 2020; 10:4378. [PMID: 32127648 PMCID: PMC7054425 DOI: 10.1038/s41598-020-61336-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Andreas Czech
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany.
| | - Petr V Konarev
- A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia.,National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ingrid Goebel
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg, Germany
| | - Peter R Wills
- Department of Physics, University of Auckland, Auckland, New Zealand
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany
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13
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Chukhovskii FN, Konarev PV, Volkov VV. Towards a solution of the inverse X-ray diffraction tomography challenge: theory and iterative algorithm for recovering the 3D displacement field function of Coulomb-type point defects in a crystal. Acta Crystallogr A Found Adv 2020; 76:163-171. [PMID: 32124854 DOI: 10.1107/s2053273320000145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/07/2020] [Indexed: 11/10/2022]
Abstract
The theoretical framework and a joint quasi-Newton-Levenberg-Marquardt-simulated annealing (qNLMSA) algorithm are established to treat an inverse X-ray diffraction tomography (XRDT) problem for recovering the 3D displacement field function fCtpd(r - r0) = h · u(r - r0) due to a Coulomb-type point defect (Ctpd) located at a point r0 within a crystal [h is the diffraction vector and u(r - r0) is the displacement vector]. The joint qNLMSA algorithm operates in a special sequence to optimize the XRDT target function {\cal F}\{ {\cal P} \} in a χ2 sense in order to recover the function fCtpd(r - r0) [{\cal P} is the parameter vector that characterizes the 3D function fCtpd(r - r0) in the algorithm search]. A theoretical framework based on the analytical solution of the Takagi-Taupin equations in the semi-kinematical approach is elaborated. In the case of true 2D imaging patterns (2D-IPs) with low counting statistics (noise-free), the joint qNLMSA algorithm enforces the target function {\cal F} \{ {\cal P} \} to tend towards the global minimum even if the vector {\cal P} in the search is initially chosen rather a long way from the true one.
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Affiliation(s)
- Felix N Chukhovskii
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre, Leninsky prospekt 59, Moscow 119333, Russian Federation
| | - Petr V Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre, Leninsky prospekt 59, Moscow 119333, Russian Federation
| | - Vladimir V Volkov
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre, Leninsky prospekt 59, Moscow 119333, Russian Federation
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14
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Konarev PV, Petoukhov MV, Dadinova LA, Fedorova NV, Volynsky PE, Svergun DI, Batishchev OV, Shtykova EV. BILMIX: a new approach to restore the size polydispersity and electron density profiles of lipid bilayers from liposomes using small-angle X-ray scattering data. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576719015656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Small-angle X-ray scattering (SAXS) is one of the major tools for the study of model membranes, but interpretation of the scattering data remains non-trivial. Current approaches allow the extraction of some structural parameters and the electron density profile of lipid bilayers. Here it is demonstrated that parametric modelling can be employed to determine the polydispersity of spherical or ellipsoidal vesicles and describe the electron density profile across the lipid bilayer. This approach is implemented in the computer program BILMIX. BILMIX delivers a description of the electron density of a lipid bilayer from SAXS data and simultaneously generates the corresponding size distribution of the unilamellar lipid vesicles.
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15
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Chukhovskii FN, Konarev PV, Volkov VV. X-Ray Diffraction Tomography Recovery of the 3D Displacement-Field Function of the Coulomb-Type Point Defect in a Crystal. Sci Rep 2019; 9:14216. [PMID: 31578401 PMCID: PMC6775144 DOI: 10.1038/s41598-019-50833-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/18/2019] [Indexed: 12/03/2022] Open
Abstract
A successive approach to the solution of the inverse problem of the X-ray diffraction tomography (XRDT) is proposed. It is based on the semi-kinematical solution of the dynamical Takagi–Taupin equations for the σ-polarized diffracted wave amplitude. Theoretically, the case of the Coulomb-type point defect in a single crystal Si(111) under the exact conditions of the symmetric Laue diffraction for a set of the tilted X-ray topography 2D-images (2D projections) is considered provided that the plane-parallel sample is rotated around the diffraction vector [\documentclass[12pt]{minimal}
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\begin{document}$$\bar{{\bf{2}}}$$\end{document}2¯20]. The iterative simulated annealing (SA) and quasi-Newton gradient descent (qNGD) algorithm codes are used for a recovery of the 3D displacement-field function of the Coulomb-type point defect. The computer recovery data of the 3D displacement-field function related to the one XRDT 2D projection are presented. It is proved that the semi-kinematical approach to the solution of the dynamical Takagi–Taupin equations is effective for recovering the 3D displacement-field function even for the one XRDT 2D projection.
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Affiliation(s)
- F N Chukhovskii
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia.
| | - P V Konarev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia. .,National Research Centre "Kurchatov Institute", Moscow, 123182, Russia.
| | - V V Volkov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia.
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16
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Marchenkova MA, Konarev PV, Rakitina TV, Timofeev VI, Boikova AS, Dyakova YA, Ilina KB, Korzhenevskiy DA, Yu Nikolaeva A, Pisarevsky YV, Kovalchuk MV. Dodecamers derived from the crystal structure were found in the pre-crystallization solution of the transaminase from the thermophilic bacterium Thermobaculum terrenum by small-angle X-ray scattering. J Biomol Struct Dyn 2019; 38:2939-2944. [PMID: 31347457 DOI: 10.1080/07391102.2019.1649195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The pre-crystallization solution of the transaminase from Thermobaculum terrenum (TaTT) has been studied by small-angle X-ray scattering (SAXS). Regular changes in the oligomeric composition of the protein were observed after the addition of the precipitant. Comparison of the observed oligomers with the crystal structure of TaTT (PDB ID 6GKR) shows that dodecamers may act as building blocks in the growth of transaminase single crystals. Correlating of these results to the similar X-ray studies of other proteins suggests that SAXS may be a valuable tool for searching optimum crystallization conditions. AbbreviationSAXSsmall-angle X-ray scatteringTatransaminaseTaTTtransaminase from Thermobaculum terrenumPLPpyridoxal-5'-phosphateR-PEAR-(þ)-1-phenylethylamineBCATbranched-chain amino acid aminotransferaseDAATD-aminoacid aminotransferaseR-TAR-amine:pyruvate transaminaseCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Margarita A Marchenkova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Petr V Konarev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Tatiana V Rakitina
- National Research Centre 'Kurchatov Institute', Moscow, Russian Federation.,Shemyakin - Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Hormonal Regulation Proteins, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Anastasiia S Boikova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Yulia A Dyakova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Kseniia B Ilina
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | | | - Alena Yu Nikolaeva
- National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Yurii V Pisarevsky
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Mikhail V Kovalchuk
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation.,St. Petersburg State University, St. Petersburg, Russian Federation
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17
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Czech A, Konarev PV, Goebel I, Svergun DI, Wills PR, Ignatova Z. Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes. Sci Rep 2019; 9:2465. [PMID: 30792490 PMCID: PMC6384910 DOI: 10.1038/s41598-019-39213-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
Misfolding and aggregation of prion protein (PrP) causes neurodegenerative diseases like Creutzfeldt-Jakob disease (CJD) and scrapie. Besides the consensus that spontaneous conversion of normal cellular PrPC into misfolded and aggregating PrPSc is the central event in prion disease, an alternative hypothesis suggests the generation of pathological PrPSc by rare translational frameshifting events in the octa-repeat domain of the PrP mRNA. Ribosomal frameshifting most commonly relies on a slippery site and an adjacent stable RNA structure to stall translating ribosome. Hence, it is crucial to unravel the secondary structure of the octa-repeat domain of PrP mRNA. Each of the five octa-repeats contains a motif (GGCGGUGGUGGCUGGG) which alone in vitro forms a G-quadruplex. Since the propensity of mRNA to form secondary structure depends on the sequence context, we set to determine the structure of the complete octa-repeat region. We assessed the structure of full-length octa-repeat domain of PrP mRNA using dynamic light scattering (DLS), small angle X-ray scattering (SAXS), circular dichroism (CD) spectroscopy and selective 2'-hydroxyl acylation analysis by primer extension (SHAPE). Our data show that the PrP octa-repeat mRNA forms stable A-helical hairpins with no evidence of G-quadruplex structure even in the presence of G-quadruplex stabilizing agents.
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Affiliation(s)
- Andreas Czech
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany.
| | - Petr V Konarev
- A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
- National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ingrid Goebel
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg, Germany
| | - Peter R Wills
- Department of Physics, University of Auckland, Auckland, New Zealand
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany
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18
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Boyko KM, Baymukhametov TN, Chesnokov YM, Hons M, Lushchekina SV, Konarev PV, Lipkin AV, Vasiliev AL, Masson P, Popov VO, Kovalchuk MV. 3D structure of the natural tetrameric form of human butyrylcholinesterase as revealed by cryoEM, SAXS and MD. Biochimie 2019; 156:196-205. [DOI: 10.1016/j.biochi.2018.10.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 12/13/2022]
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19
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Kovalchuk MV, Boikova AS, Dyakova YA, Ilina KB, Konarev PV, Kryukova AE, Marchenkova MA, Pisarevsky YV, Timofeev VI. Pre-crystallization phase formation of thermolysin hexamers in solution close to crystallization conditions. J Biomol Struct Dyn 2018; 37:3058-3064. [DOI: 10.1080/07391102.2018.1507839] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Mikhail V. Kovalchuk
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
- St. Petersburg State University, St. Petersburg, Russian Federation
| | - Anastasiia S. Boikova
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Yulia A. Dyakova
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Kseniia B. Ilina
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Petr V. Konarev
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Alyona E. Kryukova
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Margarita A. Marchenkova
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Yurii V. Pisarevsky
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir I. Timofeev
- National Research Centre “Kurchatov Institute”, Moscow, Russian Federation
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russian Federation
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20
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Konarev PV, Svergun DI. Direct shape determination of intermediates in evolving macromolecular solutions from small-angle scattering data. IUCrJ 2018; 5:402-409. [PMID: 30002841 PMCID: PMC6038953 DOI: 10.1107/s2052252518005900] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
Many important biological processes like amyloid formation, viral assembly etc. can be monitored in vitro. Small-angle X-ray scattering (SAXS) is one of the most effective techniques to structurally characterize these processes in solution. For monodisperse systems and some oligomeric mixtures, low-resolution shapes can be determined ab initio from the SAXS data, but for evolving systems, such analysis is hampered by the presence of multiple species and no direct reconstruction procedures are available. The authors consider a frequently occurring case where the scattering from the initial and final states of the process are known but there exists a major (unknown) intermediate component. A method is presented to directly reconstruct the low-resolution shape of this transient component together with its volume fractions from multiple scattering patterns recorded from an evolving system. The method is implemented in the computer program DAMMIX freely available to academic users and its effectiveness is illustrated in several synthetic and experimental examples.
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Affiliation(s)
- Petr V. Konarev
- Laboratory of Reflectometry and Small-angle Scattering, A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky pr. 59, Moscow 119333, Russian Federation
- National Research Centre ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow 123182, Russian Federation
| | - Dmitri I. Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg 22607, Germany
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21
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Cordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV. Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor. ACS Chem Biol 2018; 13:1235-1242. [PMID: 29562136 DOI: 10.1021/acschembio.8b00029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selective base pairing is the foundation of DNA recognition. Here, we elucidate the molecular and structural details of a FRET-based two-component molecular beacon relying on steady-state fluorescence spectroscopy, small-angle X-ray scattering (SAXS), microscale thermophoresis (MST), and differential electrophoretic mobility. This molecular beacon was designed to detect the most common fusion sequences causing chronic myeloid leukemia, e14a2 and e13a2. The emission spectra indicate that the self-assembly of the different components of the biosensor occurs sequentially, triggered by the fully complementary target. We further assessed the structural alterations leading to the specific fluorescence FRET signature by SAXS, MST, and the differential electrophoretic mobility, where the size range observed is consistent with hybridization and formation of a 1:1:1 complex for the probe in the presence of the complementary target and revelator. These results highlight the importance of different techniques to explore conformational DNA changes in solution and its potential to design and characterize molecular biosensors for genetic disease diagnosis.
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Affiliation(s)
- Mílton Cordeiro
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
- LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Ana Rita Otrelo-Cardoso
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Hamburg, Germany, 22067
| | - Petr V. Konarev
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Hamburg, Germany, 22067
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, Leninsky prospect 59, 119333 Moscow, Russia
- National Research Centre “Kurchatov Institute”, pl. Kurchatova 1, 123182 Moscow, Russia
| | - João Carlos Lima
- LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Teresa Santos-Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Pedro Viana Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
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22
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Adinolfi S, Puglisi R, Crack JC, Iannuzzi C, Dal Piaz F, Konarev PV, Svergun DI, Martin S, Le Brun NE, Pastore A. The Molecular Bases of the Dual Regulation of Bacterial Iron Sulfur Cluster Biogenesis by CyaY and IscX. Front Mol Biosci 2018; 4:97. [PMID: 29457004 PMCID: PMC5801593 DOI: 10.3389/fmolb.2017.00097] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 12/22/2017] [Indexed: 12/11/2022] Open
Abstract
IscX (or YfhJ) is a protein of unknown function which takes part in the iron-sulfur cluster assembly machinery, a highly specialized and essential metabolic pathway. IscX binds to iron with low affinity and interacts with IscS, the desulfurase central to cluster assembly. Previous studies have suggested a competition between IscX and CyaY, the bacterial ortholog of frataxin, for the same binding surface of IscS. This competition could suggest a link between the two proteins with a functional significance. Using a hybrid approach based on nuclear magnetic resonance, small angle scattering and biochemical methods, we show here that IscX is a modulator of the inhibitory properties of CyaY: by competing for the same site on IscS, the presence of IscX rescues the rates of enzymatic cluster formation which are inhibited by CyaY. The effect is stronger at low iron concentrations, whereas it becomes negligible at high iron concentrations. These results strongly suggest the mechanism of the dual regulation of iron sulfur cluster assembly under the control of iron as the effector.
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Affiliation(s)
| | - Rita Puglisi
- The Wohl Institute, King's College London, London, United Kingdom
| | - Jason C Crack
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Clara Iannuzzi
- The Wohl Institute, King's College London, London, United Kingdom.,DBBGP, Università degli Studi della Campania "L. Vanvitelli,", Naples, Italy
| | - Fabrizio Dal Piaz
- Dipartimento di Medicina, Chirurgia e Odontoiatria "Scuola Medica Salernitana"/DIPMED, Universita' di Salerno, Fisciano, Italy
| | - Petr V Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia.,National Research Centre "Kurchatov Institute, ", Moscow, Russia
| | | | | | - Nick E Le Brun
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Annalisa Pastore
- The Wohl Institute, King's College London, London, United Kingdom.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
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23
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Signorino G, Covaceuszach S, Bozzi M, Hübner W, Mönkemöller V, Konarev PV, Cassetta A, Brancaccio A, Sciandra F. Cover Image, Volume 39, Issue 2. Hum Mutat 2018. [DOI: 10.1002/humu.23391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Signorino G, Covaceuszach S, Bozzi M, Hübner W, Mönkemöller V, Konarev PV, Cassetta A, Brancaccio A, Sciandra F. A dystroglycan mutation (p.Cys667Phe) associated to muscle-eye-brain disease with multicystic leucodystrophy results in ER-retention of the mutant protein. Hum Mutat 2017; 39:266-280. [PMID: 29134705 DOI: 10.1002/humu.23370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/13/2017] [Accepted: 11/06/2017] [Indexed: 01/11/2023]
Abstract
Dystroglycan (DG) is a cell adhesion complex composed by two subunits, the highly glycosylated α-DG and the transmembrane β-DG. In skeletal muscle, DG is involved in dystroglycanopathies, a group of heterogeneous muscular dystrophies characterized by a reduced glycosylation of α-DG. The genes mutated in secondary dystroglycanopathies are involved in the synthesis of O-mannosyl glycans and in the O-mannosylation pathway of α-DG. Mutations in the DG gene (DAG1), causing primary dystroglycanopathies, destabilize the α-DG core protein influencing its binding to modifying enzymes. Recently, a homozygous mutation (p.Cys699Phe) hitting the β-DG ectodomain has been identified in a patient affected by muscle-eye-brain disease with multicystic leucodystrophy, suggesting that other mechanisms than hypoglycosylation of α-DG could be implicated in dystroglycanopathies. Herein, we have characterized the DG murine mutant counterpart by transfection in cellular systems and high-resolution microscopy. We observed that the mutation alters the DG processing leading to retention of its uncleaved precursor in the endoplasmic reticulum. Accordingly, small-angle X-ray scattering data, corroborated by biochemical and biophysical experiments, revealed that the mutation provokes an alteration in the β-DG ectodomain overall folding, resulting in disulfide-associated oligomerization. Our data provide the first evidence of a novel intracellular mechanism, featuring an anomalous endoplasmic reticulum-retention, underlying dystroglycanopathy.
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Affiliation(s)
- Giulia Signorino
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy
| | | | - Manuela Bozzi
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy.,Istituto di Chimica del Riconoscimento Molecolare - CNR c/o Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Wolfgang Hübner
- Biomolecular Photonics, University of Bielefeld, Bielefeld, Germany
| | | | - Petr V Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Leninsky prospect 59, Moscow, Russia
| | - Alberto Cassetta
- Istituto di Cristallografia - CNR, Trieste Outstation, Trieste, Italy
| | - Andrea Brancaccio
- Istituto di Chimica del Riconoscimento Molecolare - CNR c/o Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy.,School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Francesca Sciandra
- Istituto di Chimica del Riconoscimento Molecolare - CNR c/o Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy
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25
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Panjkovich A, Franke D, Petoukhov MV, Konarev PV, Tuukkanen A, Mertens HDT, Kikhney AG, Hajizadeh N, Jeffries CM, Svergun DI. ATSAS 2.8 software for small-angle scattering from macromolecular solutions. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317089264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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26
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Covaceuszach S, Bozzi M, Bigotti MG, Sciandra F, Konarev PV, Brancaccio A, Cassetta A. The effect of the pathological V72I, D109N and T190M missense mutations on the molecular structure of α-dystroglycan. PLoS One 2017; 12:e0186110. [PMID: 29036200 PMCID: PMC5643065 DOI: 10.1371/journal.pone.0186110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/25/2017] [Indexed: 11/18/2022] Open
Abstract
Dystroglycan (DG) is a highly glycosylated protein complex that links the cytoskeleton with the extracellular matrix, mediating fundamental physiological functions such as mechanical stability of tissues, matrix organization and cell polarity. A crucial role in the glycosylation of the DG α subunit is played by its own N-terminal region that is required by the glycosyltransferase LARGE. Alteration in this O-glycosylation deeply impairs the high affinity binding to other extracellular matrix proteins such as laminins. Recently, three missense mutations in the gene encoding DG, mapped in the α-DG N-terminal region, were found to be responsible for hypoglycosylated states, causing congenital diseases of different severity referred as primary dystroglycanopaties.To gain insight on the molecular basis of these disorders, we investigated the crystallographic and solution structures of these pathological point mutants, namely V72I, D109N and T190M. Small Angle X-ray Scattering analysis reveals that these mutations affect the structures in solution, altering the distribution between compact and more elongated conformations. These results, supported by biochemical and biophysical assays, point to an altered structural flexibility of the mutant α-DG N-terminal region that may have repercussions on its interaction with LARGE and/or other DG-modifying enzymes, eventually reducing their catalytic efficiency.
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Affiliation(s)
| | - Manuela Bozzi
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy
- Istituto di Chimica del Riconoscimento Molecolare—CNR c/o Università Cattolica del Sacro Cuore, Roma, Italy
| | | | - Francesca Sciandra
- Istituto di Chimica del Riconoscimento Molecolare—CNR c/o Università Cattolica del Sacro Cuore, Roma, Italy
| | - Petr V. Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Andrea Brancaccio
- Istituto di Chimica del Riconoscimento Molecolare—CNR c/o Università Cattolica del Sacro Cuore, Roma, Italy
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Alberto Cassetta
- Istituto di Cristallografia–CNR, Trieste Outstation, Trieste, Italy
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27
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Filippov SK, Verbraeken B, Konarev PV, Svergun DI, Angelov B, Vishnevetskaya NS, Papadakis CM, Rogers S, Radulescu A, Courtin T, Martins JC, Starovoytova L, Hruby M, Stepanek P, Kravchenko VS, Potemkin II, Hoogenboom R. Block and Gradient Copoly(2-oxazoline) Micelles: Strikingly Different on the Inside. J Phys Chem Lett 2017; 8:3800-3804. [PMID: 28759235 DOI: 10.1021/acs.jpclett.7b01588] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Herein, we provide a direct proof for differences in the micellar structure of amphiphilic diblock and gradient copolymers, thereby unambiguously demonstrating the influence of monomer distribution along the polymer chains on the micellization behavior. The internal structure of amphiphilic block and gradient co poly(2-oxazolines) based on the hydrophilic poly(2-methyl-2-oxazoline) (PMeOx) and the hydrophobic poly(2-phenyl-2-oxazoline) (PPhOx) was studied in water and water-ethanol mixtures by small-angle X-ray scattering (SAXS), small-angle neutron scattering (SANS), static and dynamic light scattering (SLS/DLS), and 1H NMR spectroscopy. Contrast matching SANS experiments revealed that block copolymers form micelles with a uniform density profile of the core. In contrast to popular assumption, the outer part of the core of the gradient copolymer micelles has a distinctly higher density than the middle of the core. We attribute the latter finding to back-folding of chains resulting from hydrophilic-hydrophobic interactions, leading to a new type of micelles that we refer to as micelles with a "bitterball-core" structure.
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Affiliation(s)
- Sergey K Filippov
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic CZ - 162 06 Praha 1, Czech Republic
| | - Bart Verbraeken
- Department of Organic and Macromolecular Chemistry, Ghent University , Krijgslaan 281-S4, 9000 Ghent, Belgium
| | - Petr V Konarev
- Hamburg Outstation, European Molecular Biology Laboratory c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre 'Crystallography and Photonics', Russian Academy of Sciences , Leninsky prospekt 59, Moscow 119333, Russian Federation
- National Research Centre "Kurchatov Institute" , Akademika Kurchatova Place 1, Moscow 123182, Russian Federation
| | - Dmitri I Svergun
- Hamburg Outstation, European Molecular Biology Laboratory c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Borislav Angelov
- Institute of Physics, Academy of Sciences of the Czech Republic , 182 21 Praha 8, Czech Republic
| | - Natalya S Vishnevetskaya
- Technische Universität München, Physik-Department , Fachgebiet Physik weicher Materie, James-Franck-Straße 1, 85748 Garching, Germany
| | - Christine M Papadakis
- Technische Universität München, Physik-Department , Fachgebiet Physik weicher Materie, James-Franck-Straße 1, 85748 Garching, Germany
| | - Sarah Rogers
- ISIS Facility, STFC, Rutherford Appleton Laboratory , Harwell Oxford, Didcot, OX11 0QX, United Kingdom
| | - Aurel Radulescu
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science JCNS, Outstation at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Tim Courtin
- Department of Organic and Macromolecular Chemistry, Ghent University , Krijgslaan 281-S4, 9000 Ghent, Belgium
| | - José C Martins
- Department of Organic and Macromolecular Chemistry, Ghent University , Krijgslaan 281-S4, 9000 Ghent, Belgium
| | - Larisa Starovoytova
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic CZ - 162 06 Praha 1, Czech Republic
| | - Martin Hruby
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic CZ - 162 06 Praha 1, Czech Republic
| | - Petr Stepanek
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic CZ - 162 06 Praha 1, Czech Republic
| | - Vitaly S Kravchenko
- Physics Department, Lomonosov Moscow State University , Moscow 119991, Russian Federation
| | - Igor I Potemkin
- Physics Department, Lomonosov Moscow State University , Moscow 119991, Russian Federation
- National Research South Ural State University , Chelyabinsk 454080, Russian Federation
| | - Richard Hoogenboom
- Department of Organic and Macromolecular Chemistry, Ghent University , Krijgslaan 281-S4, 9000 Ghent, Belgium
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28
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Boikova AS, Dyakova YA, Ilina KB, Konarev PV, Kryukova AE, Kuklin AI, Marchenkova MA, Nabatov BV, Blagov AE, Pisarevsky YV, Kovalchuk MV. Octamer formation in lysozyme solutions at the initial crystallization stage detected by small-angle neutron scattering. Acta Crystallogr D Struct Biol 2017; 73:591-599. [PMID: 28695859 DOI: 10.1107/s2059798317007422] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/19/2017] [Indexed: 11/10/2022]
Abstract
Solutions of lysozyme in heavy water were studied by small-angle neutron scattering (SANS) at concentrations of 40, 20 and 10 mg ml-1 with and without the addition of precipitant, and at temperatures of 10, 20 and 30°C. In addition to the expected protein monomers, dimeric and octameric species were identified in solutions at the maximum concentration and close to the optimal conditions for crystallization. An optimal temperature for octamer formation was identified and both deviation from this temperature and a reduction in protein concentration led to a significant decrease in the volume fractions of octamers detected. In the absence of precipitant, only monomers and a minor fraction of dimers are present in solution.
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Affiliation(s)
- Anastasiia S Boikova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Yulia A Dyakova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Kseniia B Ilina
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Petr V Konarev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Alyona E Kryukova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Alexandr I Kuklin
- The Joint Institute for Nuclear Research, Joliot-Curie str. 6, Dubna 141980, Russian Federation
| | - Margarita A Marchenkova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Boris V Nabatov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Alexandr E Blagov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Yurii V Pisarevsky
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Mikhail V Kovalchuk
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
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Franke D, Petoukhov MV, Konarev PV, Panjkovich A, Tuukkanen A, Mertens HDT, Kikhney AG, Hajizadeh NR, Franklin JM, Jeffries CM, Svergun DI. ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions. J Appl Crystallogr 2017; 50:1212-1225. [PMID: 28808438 PMCID: PMC5541357 DOI: 10.1107/s1600576717007786] [Citation(s) in RCA: 953] [Impact Index Per Article: 136.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/25/2017] [Indexed: 11/16/2022] Open
Abstract
Developments and improvements of the ATSAS software suite (versions 2.5–2.8) for analysis of small-angle scattering data of biological macromolecules or nanoparticles are described. ATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment, ab initio bead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data. This article summarizes the progress made during the 2.5–2.8 ATSAS release series and highlights the latest developments. These include AMBIMETER, an assessment of the reconstruction ambiguity of experimental data; DATCLASS, a multiclass shape classification based on experimental data; SASRES, for estimating the resolution of ab initio model reconstructions; CHROMIXS, a convenient interface to analyse in-line size exclusion chromatography data; SHANUM, to evaluate the useful angular range in measured data; SREFLEX, to refine available high-resolution models using normal mode analysis; SUPALM for a rapid superposition of low- and high-resolution models; and SASPy, the ATSAS plugin for interactive modelling in PyMOL. All these features and other improvements are included in the ATSAS release 2.8, freely available for academic users from https://www.embl-hamburg.de/biosaxs/software.html.
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Affiliation(s)
- D Franke
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - M V Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany.,Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Leninsky prospect 59, 119333 Moscow, Russian Federation.,A. N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky prospect 31, 119071 Moscow, and N.N. Semenov Institute of Chemical Physics of Russian Academy of Sciences, Kosygina street 4, 119991 Moscow, Russian Federation
| | - P V Konarev
- Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Leninsky prospect 59, 119333 Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', ploshchad Kurchatova 1, 123182 Moscow, Russian Federation
| | - A Panjkovich
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - A Tuukkanen
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - H D T Mertens
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - A G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - N R Hajizadeh
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - J M Franklin
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | - C M Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - D I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
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Hastings R, de Villiers CP, Hooper C, Ormondroyd L, Pagnamenta A, Lise S, Salatino S, Knight SJL, Taylor JC, Thomson KL, Arnold L, Chatziefthimiou SD, Konarev PV, Wilmanns M, Ehler E, Ghisleni A, Gautel M, Blair E, Watkins H, Gehmlich K. Combination of Whole Genome Sequencing, Linkage, and Functional Studies Implicates a Missense Mutation in Titin as a Cause of Autosomal Dominant Cardiomyopathy With Features of Left Ventricular Noncompaction. ACTA ACUST UNITED AC 2016; 9:426-435. [PMID: 27625337 PMCID: PMC5068189 DOI: 10.1161/circgenetics.116.001431] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/31/2016] [Indexed: 11/16/2022]
Abstract
Supplemental Digital Content is available in the text. Background— High throughput next-generation sequencing techniques have made whole genome sequencing accessible in clinical practice; however, the abundance of variation in the human genomes makes the identification of a disease-causing mutation on a background of benign rare variants challenging. Methods and Results— Here we combine whole genome sequencing with linkage analysis in a 3-generation family affected by cardiomyopathy with features of autosomal dominant left ventricular noncompaction cardiomyopathy. A missense mutation in the giant protein titin is the only plausible disease-causing variant that segregates with disease among the 7 surviving affected individuals, with interrogation of the entire genome excluding other potential causes. This A178D missense mutation, affecting a conserved residue in the second immunoglobulin-like domain of titin, was introduced in a bacterially expressed recombinant protein fragment and biophysically characterized in comparison to its wild-type counterpart. Multiple experiments, including size exclusion chromatography, small-angle x ray scattering, and circular dichroism spectroscopy suggest partial unfolding and domain destabilization in the presence of the mutation. Moreover, binding experiments in mammalian cells show that the mutation markedly impairs binding to the titin ligand telethonin. Conclusions— Here we present genetic and functional evidence implicating the novel A178D missense mutation in titin as the cause of a highly penetrant familial cardiomyopathy with features of left ventricular noncompaction. This expands the spectrum of titin’s roles in cardiomyopathies. It furthermore highlights that rare titin missense variants, currently often ignored or left uninterpreted, should be considered to be relevant for cardiomyopathies and can be identified by the approach presented here.
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Konarev PV, Petoukhov MV, Svergun DI. Rapid automated superposition of shapes and macromolecular models using spherical harmonics. J Appl Crystallogr 2016; 49:953-960. [PMID: 27275142 PMCID: PMC4886985 DOI: 10.1107/s1600576716005793] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 04/07/2016] [Indexed: 01/20/2023] Open
Abstract
A rapid algorithm to superimpose macromolecular models in Fourier space is proposed and implemented (SUPALM). The method uses a normalized integrated cross-term of the scattering amplitudes as a proximity measure between two three-dimensional objects. The reciprocal-space algorithm allows for direct matching of heterogeneous objects including high- and low-resolution models represented by atomic coordinates, beads or dummy residue chains as well as electron microscopy density maps and inhomogeneous multi-phase models (e.g. of protein-nucleic acid complexes). Using spherical harmonics for the computation of the amplitudes, the method is up to an order of magnitude faster than the real-space algorithm implemented in SUPCOMB by Kozin & Svergun [J. Appl. Cryst. (2001 ▸), 34, 33-41]. The utility of the new method is demonstrated in a number of test cases and compared with the results of SUPCOMB. The spherical harmonics algorithm is best suited for low-resolution shape models, e.g. those provided by solution scattering experiments, but also facilitates a rapid cross-validation against structural models obtained by other methods.
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Affiliation(s)
- Petr V. Konarev
- Laboratory of Reflectometry and Small-Angle Scattering, A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre ‘Crystallography and Photonics’, Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Maxim V. Petoukhov
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg, 22607, Germany
| | - Dmitri I. Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg, 22607, Germany
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32
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Dadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI. X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 2016; 11:e0156105. [PMID: 27227414 PMCID: PMC4881948 DOI: 10.1371/journal.pone.0156105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 05/08/2016] [Indexed: 11/21/2022] Open
Abstract
The structural analyses of four metabolic enzymes that maintain and regulate the stationary growth phase of Escherichia coli have been performed primarily drawing on the results obtained from solution small angle X-ray scattering (SAXS) and other structural techniques. The proteins are (i) class I fructose-1,6-bisphosphate aldolase (FbaB); (ii) inorganic pyrophosphatase (PPase); (iii) 5-keto-4-deoxyuronate isomerase (KduI); and (iv) glutamate decarboxylase (GadA). The enzyme FbaB, that until now had an unknown structure, is predicted to fold into a TIM-barrel motif that form globular protomers which SAXS experiments show associate into decameric assemblies. In agreement with previously reported crystal structures, PPase forms hexamers in solution that are similar to the previously reported X-ray crystal structure. Both KduI and GadA that are responsible for carbohydrate (pectin) metabolism and acid stress responses, respectively, form polydisperse mixtures consisting of different oligomeric states. Overall the SAXS experiments yield additional insights into shape and organization of these metabolic enzymes and further demonstrate the utility of hybrid methods, i.e., solution SAXS combined with X-ray crystallography, bioinformatics and predictive 3D-structural modeling, as tools to enrich structural studies. The results highlight the structural complexity that the protein components of metabolic networks may adopt which cannot be fully captured using individual structural biology techniques.
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Affiliation(s)
- Liubov A. Dadinova
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- M.V. Lomonosov Moscow State University, Physics Department, Moscow, Russia
| | - Eleonora V. Shtykova
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Petr V. Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
| | - Elena V. Rodina
- M.V. Lomonosov Moscow State University, Chemistry Department, Moscow, Russia
| | - Natalia E. Snalina
- M.V. Lomonosov Moscow State University, Chemistry Department, Moscow, Russia
| | - Natalia N. Vorobyeva
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- M.V. Lomonosov Moscow State University, Chemistry Department, Moscow, Russia
| | - Svetlana A. Kurilova
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Tatyana I. Nazarova
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
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Gráczer É, Szimler T, Garamszegi A, Konarev PV, Lábas A, Oláh J, Palló A, Svergun DI, Merli A, Závodszky P, Weiss MS, Vas M. Dual Role of the Active Site Residues of Thermus thermophilus 3-Isopropylmalate Dehydrogenase: Chemical Catalysis and Domain Closure. Biochemistry 2016; 55:560-74. [PMID: 26731489 DOI: 10.1021/acs.biochem.5b00839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The key active site residues K185, Y139, D217, D241, D245, and N102 of Thermus thermophilus 3-isopropylmalate dehydrogenase (Tt-IPMDH) have been replaced, one by one, with Ala. A drastic decrease in the kcat value (0.06% compared to that of the wild-type enzyme) has been observed for the K185A and D241A mutants. Similarly, the catalytic interactions (Km values) of these two mutants with the substrate IPM are weakened by more than 1 order of magnitude. The other mutants retained some (1-13%) of the catalytic activity of the wild-type enzyme and do not exhibit appreciable changes in the substrate Km values. The pH dependence of the wild-type enzyme activity (pK = 7.4) is shifted toward higher values for mutants K185A and D241A (pK values of 8.4 and 8.5, respectively). For the other mutants, smaller changes have been observed. Consequently, K185 and D241 may constitute a proton relay system that can assist in the abstraction of a proton from the OH group of IPM during catalysis. Molecular dynamics simulations provide strong support for the neutral character of K185 in the resting state of the enzyme, which implies that K185 abstracts the proton from the substrate and D241 assists the process via electrostatic interactions with K185. Quantum mechanics/molecular mechanics calculations revealed a significant increase in the activation energy of the hydride transfer of the redox step for both D217A and D241A mutants. Crystal structure analysis of the molecular contacts of the investigated residues in the enzyme-substrate complex revealed their additional importance (in particular that of K185, D217, and D241) in stabilizing the domain-closed active conformation. In accordance with this, small-angle X-ray scattering measurements indicated the complete absence of domain closure in the cases of D217A and D241A mutants, while only partial domain closure could be detected for the other mutants. This suggests that the same residues that are important for catalysis are also essential for inducing domain closure.
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Affiliation(s)
- Éva Gráczer
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| | - Tamás Szimler
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| | - Anita Garamszegi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| | - Petr V Konarev
- European Molecular Biology Laboratory , Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Anikó Lábas
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics , Gellért tér 4., H-1111 Budapest, Hungary
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics , Gellért tér 4., H-1111 Budapest, Hungary
| | - Anna Palló
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| | - Dmitri I Svergun
- European Molecular Biology Laboratory , Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Angelo Merli
- Dipartimento di Bioscienze, Universitá degli Studi di Parma , Viale G.P. Usberti 23/A, I-43100 Parma, Italy
| | - Péter Závodszky
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin für Materialien und Energie , Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Mária Vas
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
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Nowak E, Miller JT, Bona MK, Studnicka J, Konarev PV, Szczepanowski RH, Potrzebowski W, Svergun DI, Jurkowski J, Bujnicki J, Grice SFL, Nowotny M. Structure and mechanism of reverse transcriptases. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315096199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Malyutin AG, Cheng H, Sanchez-Felix OR, Carlson K, Stein BD, Konarev PV, Svergun DI, Dragnea B, Bronstein LM. Coat Protein-Dependent Behavior of Poly(ethylene glycol) Tails in Iron Oxide Core Virus-like Nanoparticles. ACS Appl Mater Interfaces 2015; 7:12089-12098. [PMID: 25989427 DOI: 10.1021/acsami.5b02278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Here we explore the formation of virus-like nanoparticles (VNPs) utilizing 22-24 nm iron oxide nanoparticles (NPs) as cores and proteins derived from viral capsids of brome mosaic virus (BMV) or hepatitis B virus (HBV) as shells. To accomplish that, hydrophobic FeO/Fe3O4 NPs prepared by thermal decomposition of iron oleate were coated with poly(maleic acid-alt-octadecene) modified with poly(ethylene glycol) (PEG) tails of different lengths and grafting densities. MRI studies show high r2/r1 relaxivity ratios of these NPs that are practically independent of the polymer coating type. The versatility and flexibility of the viral capsid protein are on display as they readily form shells that exceed their native size. The location of the long PEG tails upon shell formation was investigated by electron microscopy and small-angle X-ray scattering. PEG tails were located differently in the BMV and HBV VNPs, with the BMV VNPs preferentially entrapping the tails in the interior and the HBV VNPs allowing the tails to extend through the capsid, which highlights the differences between intersubunit interactions in these two icosahedral viruses. The robustness of the assembly reaction and the protruding PEG tails, potentially useful in modulating the immune response, make the systems introduced here a promising platform for biomedical applications.
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Affiliation(s)
- Andrey G Malyutin
- †Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Hu Cheng
- §Department of Psychological and Brain Sciences, Indiana University, 1101 East Tenth Street, Bloomington, Indiana 47403, United States
| | - Olivia R Sanchez-Felix
- †Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Kenneth Carlson
- †Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Barry D Stein
- ∥Department of Biology, Indiana University, 1001 East Third Street, Bloomington, Indiana 47405, United States
| | - Petr V Konarev
- ‡EMBL, Hamburg Outstation, Notkestraße 85, D-22603 Hamburg, Germany
| | - Dmitri I Svergun
- ‡EMBL, Hamburg Outstation, Notkestraße 85, D-22603 Hamburg, Germany
| | - Bogdan Dragnea
- †Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lyudmila M Bronstein
- †Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
- #Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Konarev PV, Svergun DI. A posteriori determination of the useful data range for small-angle scattering experiments on dilute monodisperse systems. IUCrJ 2015; 2:352-360. [PMID: 25995844 PMCID: PMC4420545 DOI: 10.1107/s2052252515005163] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 03/13/2015] [Indexed: 05/29/2023]
Abstract
Small-angle X-ray and neutron scattering (SAXS and SANS) experiments on solutions provide rapidly decaying scattering curves, often with a poor signal-to-noise ratio, especially at higher angles. On modern instruments, the noise is partially compensated for by oversampling, thanks to the fact that the angular increment in the data is small compared with that needed to describe adequately the local behaviour and features of the scattering curve. Given a (noisy) experimental data set, an important question arises as to which part of the data still contains useful information and should be taken into account for the interpretation and model building. Here, it is demonstrated that, for monodisperse systems, the useful experimental data range is defined by the number of meaningful Shannon channels that can be determined from the data set. An algorithm to determine this number and thus the data range is developed, and it is tested on a number of simulated data sets with various noise levels and with different degrees of oversampling, corresponding to typical SAXS/SANS experiments. The method is implemented in a computer program and examples of its application to analyse the experimental data recorded under various conditions are presented. The program can be employed to discard experimental data containing no useful information in automated pipelines, in modelling procedures, and for data deposition or publication. The software is freely accessible to academic users.
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Affiliation(s)
- Petr V. Konarev
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg 22607, Germany
- Laboratory of Reflectometry and Small-angle Scattering, Institute of Crystallography of the Russian Academy of Sciences, Leninsky prospekt 59, Moscow 119333, Russian Federation
| | - Dmitri I. Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg 22607, Germany
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37
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Song JG, Kostan J, Drepper F, Knapp B, de Almeida Ribeiro E, Konarev PV, Grishkovskaya I, Wiche G, Gregor M, Svergun DI, Warscheid B, Djinović-Carugo K. Structural insights into Ca2+-calmodulin regulation of Plectin 1a-integrin β4 interaction in hemidesmosomes. Structure 2015; 23:558-570. [PMID: 25703379 PMCID: PMC4353693 DOI: 10.1016/j.str.2015.01.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/24/2014] [Accepted: 01/06/2015] [Indexed: 02/02/2023]
Abstract
The mechanical stability of epithelial cells, which protect organisms from harmful external factors, is maintained by hemidesmosomes via the interaction between plectin 1a (P1a) and integrin α6β4. Binding of calcium-calmodulin (Ca2+-CaM) to P1a together with phosphorylation of integrin β4 disrupts this complex, resulting in disassembly of hemidesmosomes. We present structures of the P1a actin binding domain either in complex with the N-ter lobe of Ca2+-CaM or with the first pair of integrin β4 fibronectin domains. Ca2+-CaM binds to the N-ter isoform-specific tail of P1a in a unique manner, via its N-ter lobe in an extended conformation. Structural, cell biology, and biochemical studies suggest the following model: binding of Ca2+-CaM to an intrinsically disordered N-ter segment of plectin converts it to an α helix, which repositions calmodulin to displace integrin β4 by steric repulsion. This model could serve as a blueprint for studies aimed at understanding how Ca2+-CaM or EF-hand motifs regulate F-actin-based cytoskeleton. Calmodulin binds to plectin 1a via its N-terminal lobe in an extended conformation The disordered N-ter tail of plectin 1a folds in an α helix upon calmodulin binding Suitably positioned calmodulin displaces integrin β4 from complex with plectin 1a
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Affiliation(s)
- Jae-Geun Song
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Julius Kostan
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Friedel Drepper
- Department of Functional Proteomics and Biochemistry, Institute of Biology II and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Bettina Knapp
- Department of Functional Proteomics and Biochemistry, Institute of Biology II and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Euripedes de Almeida Ribeiro
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Petr V Konarev
- EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Gerhard Wiche
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria
| | - Martin Gregor
- Department of Integrative Biology, Institute of Molecular Genetics of the ASCR, Vídeňská 1083, Prague 4 CZ-14220, Czech Republic
| | - Dmitri I Svergun
- EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Bettina Warscheid
- Department of Functional Proteomics and Biochemistry, Institute of Biology II and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Campus Vienna Biocenter 5, A-1030 Vienna, Austria; Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia.
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38
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Faggiano S, Menon RP, Kelly GP, Todi SV, Scaglione KM, Konarev PV, Svergun DI, Paulson HL, Pastore A. Allosteric regulation of deubiquitylase activity through ubiquitination. Front Mol Biosci 2015; 2:2. [PMID: 25988170 PMCID: PMC4428445 DOI: 10.3389/fmolb.2015.00002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/07/2015] [Indexed: 12/28/2022] Open
Abstract
Ataxin-3, the protein responsible for spinocerebellar ataxia type-3, is a cysteine protease that specifically cleaves poly-ubiquitin chains and participates in the ubiquitin proteasome pathway. The enzymatic activity resides in the N-terminal Josephin domain. An unusual feature of ataxin-3 is its low enzymatic activity especially for mono-ubiquitinated substrates and short ubiquitin chains. However, specific ubiquitination at lysine 117 in the Josephin domain activates ataxin-3 through an unknown mechanism. Here, we investigate the effects of K117 ubiquitination on the structure and enzymatic activity of the protein. We show that covalently linked ubiquitin rests on the Josephin domain, forming a compact globular moiety and occupying a ubiquitin binding site previously thought to be essential for substrate recognition. In doing so, ubiquitination enhances enzymatic activity by locking the enzyme in an activated state. Our results indicate that ubiquitin functions both as a substrate and as an allosteric regulatory factor. We provide a novel example in which a conformational switch controls the activity of an enzyme that mediates deubiquitination.
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Affiliation(s)
- Serena Faggiano
- National Institute for Medical Research, Medical Research Council London, UK
| | - Rajesh P Menon
- National Institute for Medical Research, Medical Research Council London, UK
| | - Geoff P Kelly
- Medical Research Council Biomedical NMR Centre, National Institute for Medical Research, Medical Research Council London, UK
| | - Sokol V Todi
- Department of Pharmacology and Department of Neurology, Wayne State University School of Medicine Detroit, MI, USA
| | - K Matthew Scaglione
- Department of Biochemistry and The Neuroscience Research Center, Medical College of Wisconsin Milwaukee, WI, USA
| | - Petr V Konarev
- European Molecular Biology Laboratory Hamburg, Germany ; Laboratory of Reflectometry and Small-Angle Scattering, Institute of Crystallography Russian Academy of Sciences Moscow, Russia
| | | | - Henry L Paulson
- Department of Neurology, University of Michigan Medical School Ann Arbor, MI, USA
| | - Annalisa Pastore
- Department of Clinical Neuroscience, King's College London London, UK
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39
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Covaceuszach S, Konarev PV, Cassetta A, Paoletti F, Svergun DI, Lamba D, Cattaneo A. The conundrum of the high-affinity NGF binding site formation unveiled? Biophys J 2015; 108:687-97. [PMID: 25650935 PMCID: PMC4317559 DOI: 10.1016/j.bpj.2014.11.3485] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/05/2014] [Accepted: 11/07/2014] [Indexed: 11/15/2022] Open
Abstract
The homodimer NGF (nerve growth factor) exerts its neuronal activity upon binding to either or both distinct transmembrane receptors TrkA and p75(NTR). Functionally relevant interactions between NGF and these receptors have been proposed, on the basis of binding and signaling experiments. Namely, a ternary TrkA/NGF/p75(NTR) complex is assumed to be crucial for the formation of the so-called high-affinity NGF binding sites. However, the existence, on the cell surface, of direct extracellular interactions is still a matter of controversy. Here, supported by a small-angle x-ray scattering solution study of human NGF, we propose that it is the oligomerization state of the secreted NGF that may drive the formation of the ternary heterocomplex. Our data demonstrate the occurrence in solution of a concentration-dependent distribution of dimers and dimer of dimers. A head-to-head molecular assembly configuration of the NGF dimer of dimers has been validated. Overall, these findings prompted us to suggest a new, to our knowledge, model for the transient ternary heterocomplex, i.e., a TrkA/NGF/p75(NTR) ligand/receptors molecular assembly with a (2:4:2) stoichiometry. This model would neatly solve the problem posed by the unconventional orientation of p75(NTR) with respect to TrkA, as being found in the crystal structures of the TrkA/NGF and p75(NTR)/NGF complexes.
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Affiliation(s)
- Sonia Covaceuszach
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy
| | - Petr V Konarev
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany; Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia
| | - Alberto Cassetta
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy
| | | | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | - Doriano Lamba
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy.
| | - Antonino Cattaneo
- European Brain Research Institute, Roma, Italy; Scuola Normale Superiore, Pisa, Italy.
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40
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Ribeiro EDA, Pinotsis N, Ghisleni A, Salmazo A, Konarev PV, Kostan J, Sjöblom B, Schreiner C, Polyansky AA, Gkougkoulia EA, Holt MR, Aachmann FL, Zagrović B, Bordignon E, Pirker KF, Svergun DI, Gautel M, Djinović-Carugo K. The structure and regulation of human muscle α-actinin. Cell 2014; 159:1447-60. [PMID: 25433700 PMCID: PMC4259493 DOI: 10.1016/j.cell.2014.10.056] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 10/01/2014] [Accepted: 10/24/2014] [Indexed: 11/29/2022]
Abstract
The spectrin superfamily of proteins plays key roles in assembling the actin cytoskeleton in various cell types, crosslinks actin filaments, and acts as scaffolds for the assembly of large protein complexes involved in structural integrity and mechanosensation, as well as cell signaling. α-actinins in particular are the major actin crosslinkers in muscle Z-disks, focal adhesions, and actin stress fibers. We report a complete high-resolution structure of the 200 kDa α-actinin-2 dimer from striated muscle and explore its functional implications on the biochemical and cellular level. The structure provides insight into the phosphoinositide-based mechanism controlling its interaction with sarcomeric proteins such as titin, lays a foundation for studying the impact of pathogenic mutations at molecular resolution, and is likely to be broadly relevant for the regulation of spectrin-like proteins. Structure of human α-actinin-2 in an autoinhibited closed conformation Facilitation of PIP2-induced allosteric modulation for opening and titin binding Essentiality of structural flexibility for crosslinking antiparallel F-actin Relevance for the intramolecular pseudoligand regulation mechanism of the spectrin family
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Affiliation(s)
- Euripedes de Almeida Ribeiro
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Nikos Pinotsis
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Andrea Ghisleni
- British Heart Foundation Centre of Research Excellence, Randall Division for Cell and Molecular Biophysics and Cardiovascular Division, King's College London, London SE1 1UL, UK
| | - Anita Salmazo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Petr V Konarev
- European Molecular Biology Laboratory, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22603 Hamburg, Germany
| | - Julius Kostan
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Björn Sjöblom
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Claudia Schreiner
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria; M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Eirini A Gkougkoulia
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Mark R Holt
- British Heart Foundation Centre of Research Excellence, Randall Division for Cell and Molecular Biophysics and Cardiovascular Division, King's College London, London SE1 1UL, UK
| | - Finn L Aachmann
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands vei 6/8, 7491 Trondheim, Norway
| | - Bojan Zagrović
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Enrica Bordignon
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland; Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Katharina F Pirker
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22603 Hamburg, Germany
| | - Mathias Gautel
- British Heart Foundation Centre of Research Excellence, Randall Division for Cell and Molecular Biophysics and Cardiovascular Division, King's College London, London SE1 1UL, UK.
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria; Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia.
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41
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Bonanomi M, Mazzucchelli S, D’Urzo A, Nardini M, Konarev PV, Invernizzi G, Svergun DI, Vanoni M, Regonesi ME, Tortora P. Interactions of ataxin-3 with its molecular partners in the protein machinery that sorts protein aggregates to the aggresome. Int J Biochem Cell Biol 2014; 51:58-64. [DOI: 10.1016/j.biocel.2014.03.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 03/05/2014] [Accepted: 03/20/2014] [Indexed: 01/09/2023]
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42
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Konarev PV, Kachalova GS, Ryazanova AY, Kubareva EA, Karyagina AS, Bartunik HD, Svergun DI. Flexibility of the linker between the domains of DNA methyltransferase SsoII revealed by small-angle X-ray scattering: implications for transcription regulation in SsoII restriction-modification system. PLoS One 2014; 9:e93453. [PMID: 24710319 PMCID: PMC3978073 DOI: 10.1371/journal.pone.0093453] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/03/2014] [Indexed: 11/18/2022] Open
Abstract
(Cytosine-5)-DNA methyltransferase SsoII (M.SsoII) consists of a methyltransferase domain (residues 72-379) and an N-terminal region (residues 1-71) which regulates transcription in SsoII restriction-modification system. Small-angle X-ray scattering (SAXS) is employed here to study the low resolution structure of M.SsoII and its complex with DNA containing the methylation site. The shapes reconstructed ab initio from the SAXS data reveal two distinct protein domains of unequal size. The larger domain matches the crystallographic structure of a homologous DNA methyltransferase HhaI (M.HhaI), and the cleft in this domain is occupied by DNA in the model of the complex reconstructed from the SAXS data. This larger domain can thus be identified as the methyltransferase domain whereas the other domain represents the N-terminal region. Homology modeling of the M.SsoII structure is performed by using the model of M.HhaI for the methyltransferase domain and representing the N-terminal region either as a flexible chain of dummy residues or as a rigid structure of a homologous protein (phage 434 repressor) connected to the methyltransferase domain by a short flexible linker. Both models are compatible with the SAXS data and demonstrate high mobility of the N-terminal region. The linker flexibility might play an important role in the function of M.SsoII as a transcription factor.
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Affiliation(s)
- Petr V. Konarev
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | | | - Alexandra Yu Ryazanova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna S. Karyagina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Gamaleya Institute of Epidemiology and Microbiology, Moscow, Russia
- Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Hans D. Bartunik
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
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43
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Sergeeva O, Vlasov PS, Domnina NS, Bogomolova A, Konarev PV, Svergun DI, Walterova Z, Horsky J, Stepanek P, Filippov SK. Novel thermosensitive telechelic PEGs with antioxidant activity: synthesis, molecular properties and conformational behaviour. RSC Adv 2014. [DOI: 10.1039/c4ra06978a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We report on the tailor-made polymer conjugates, which are highly compelling for biomedical applications due to their antioxidant activity and the adjustable thermosensitive properties.
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Affiliation(s)
- Olga Sergeeva
- Institute of Chemistry
- Saint-Petersburg State University
- Russia
| | - Petr S. Vlasov
- Institute of Chemistry
- Saint-Petersburg State University
- Russia
| | - Nina S. Domnina
- Institute of Chemistry
- Saint-Petersburg State University
- Russia
| | | | | | | | | | - Jiri Horsky
- Institute of Macromolecular Chemistry
- Prague, Czech Republic
| | - Petr Stepanek
- Institute of Macromolecular Chemistry
- Prague, Czech Republic
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44
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Filippov SK, Franklin JM, Konarev PV, Chytil P, Etrych T, Bogomolova A, Dyakonova M, Papadakis CM, Radulescu A, Ulbrich K, Stepanek P, Svergun DI. Hydrolytically Degradable Polymer Micelles for Drug Delivery: A SAXS/SANS Kinetic Study. Biomacromolecules 2013; 14:4061-70. [DOI: 10.1021/bm401186z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sergey K. Filippov
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - John M. Franklin
- European Molecular
Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg, D-22603, Germany
| | - Petr V. Konarev
- European Molecular
Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg, D-22603, Germany
| | - Petr Chytil
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - Tomas Etrych
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - Anna Bogomolova
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - Margarita Dyakonova
- Technische Universität München, Physik-Department, Fachgebiet Physik weicher Materie, James-Franck-Str. 1, 85748 Garching, Germany
| | - Christine M. Papadakis
- Technische Universität München, Physik-Department, Fachgebiet Physik weicher Materie, James-Franck-Str. 1, 85748 Garching, Germany
| | - Aurel Radulescu
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science JCNS, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Karel Ulbrich
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - Petr Stepanek
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - Dmitri I. Svergun
- European Molecular
Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg, D-22603, Germany
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45
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Yan R, Konarev PV, Iannuzzi C, Adinolfi S, Roche B, Kelly G, Simon L, Martin SR, Py B, Barras F, Svergun DI, Pastore A. Ferredoxin competes with bacterial frataxin in binding to the desulfurase IscS. J Biol Chem 2013; 288:24777-87. [PMID: 23839945 PMCID: PMC3750173 DOI: 10.1074/jbc.m113.480327] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/03/2013] [Indexed: 11/06/2022] Open
Abstract
The bacterial iron-sulfur cluster (isc) operon is an essential machine that is highly conserved from bacteria to primates and responsible for iron-sulfur cluster biogenesis. Among its components are the genes for the desulfurase IscS that provides sulfur for cluster formation, and a specialized ferredoxin (Fdx) whose role is still unknown. Preliminary evidence suggests that IscS and Fdx interact but nothing is known about the binding site and the role of the interaction. Here, we have characterized the interaction using a combination of biophysical tools and mutagenesis. By modeling the Fdx·IscS complex based on experimental restraints we show that Fdx competes for the binding site of CyaY, the bacterial ortholog of frataxin and sits in a cavity close to the enzyme active site. By in vivo mutagenesis in bacteria we prove the importance of the surface of interaction for cluster formation. Our data provide the first structural insights into the role of Fdx in cluster assembly.
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Affiliation(s)
- Robert Yan
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | - Petr V. Konarev
- the European Molecular Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg D-22603, Germany, and
| | - Clara Iannuzzi
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | - Salvatore Adinolfi
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | | | - Geoff Kelly
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | - Léa Simon
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | - Stephen R. Martin
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | - Béatrice Py
- the Aix-Marseille Université and
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, UMR 7283, CNRS, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Frédéric Barras
- the Aix-Marseille Université and
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, UMR 7283, CNRS, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Dmitri I. Svergun
- the European Molecular Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg D-22603, Germany, and
| | - Annalisa Pastore
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
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46
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Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SFJ, Nowotny M. Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 2013; 41:3874-87. [PMID: 23382176 PMCID: PMC3616737 DOI: 10.1093/nar/gkt053] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/11/2013] [Accepted: 01/11/2013] [Indexed: 11/19/2022] Open
Abstract
A key step in proliferation of retroviruses is the conversion of their RNA genome to double-stranded DNA, a process catalysed by multifunctional reverse transcriptases (RTs). Dimeric and monomeric RTs have been described, the latter exemplified by the enzyme of Moloney murine leukaemia virus. However, structural information is lacking that describes the substrate binding mechanism for a monomeric RT. We report here the first crystal structure of a complex between an RNA/DNA hybrid substrate and polymerase-connection fragment of the single-subunit RT from xenotropic murine leukaemia virus-related virus, a close relative of Moloney murine leukaemia virus. A comparison with p66/p51 human immunodeficiency virus-1 RT shows that substrate binding around the polymerase active site is conserved but differs in the thumb and connection subdomains. Small-angle X-ray scattering was used to model full-length xenotropic murine leukaemia virus-related virus RT, demonstrating that its mobile RNase H domain becomes ordered in the presence of a substrate-a key difference between monomeric and dimeric RTs.
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Affiliation(s)
- Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Wojciech Potrzebowski
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Petr V. Konarev
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Jason W. Rausch
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Marion K. Bona
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Dmitri I. Svergun
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Janusz M. Bujnicki
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Stuart F. J. Le Grice
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
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47
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de Chiara C, Rees M, Menon RP, Pauwels K, Lawrence C, Konarev PV, Svergun DI, Martin SR, Chen YW, Pastore A. Self-assembly and conformational heterogeneity of the AXH domain of ataxin-1: an unusual example of a chameleon fold. Biophys J 2013; 104:1304-13. [PMID: 23528090 DOI: 10.1016/j.bpj.2013.01.048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/20/2013] [Accepted: 01/28/2013] [Indexed: 10/27/2022] Open
Abstract
Ataxin-1 is a human protein responsible for spinocerebellar ataxia type 1, a hereditary disease associated with protein aggregation and misfolding. Essential for ataxin-1 aggregation is the anomalous expansion of a polyglutamine tract near the protein N-terminus, but the sequence-wise distant AXH domain modulates and contributes to the process. The AXH domain is also involved in the nonpathologic functions of the protein, including a variety of intermolecular interactions with other cellular partners. The domain forms a globular dimer in solution and displays a dimer of dimers arrangement in the crystal asymmetric unit. Here, we have characterized the domain further by studying its behavior in the crystal and in solution. We solved two new structures of the domain crystallized under different conditions that confirm an inherent plasticity of the AXH fold. In solution, the domain is present as a complex equilibrium mixture of monomeric, dimeric, and higher molecular weight species. This behavior, together with the tendency of the AXH fold to be trapped in local conformations, and the multiplicity of protomer interfaces, makes the AXH domain an unusual example of a chameleon protein whose properties bear potential relevance for the aggregation properties of ataxin-1 and thus for disease.
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Affiliation(s)
- Cesira de Chiara
- Medical Research Council National Institute for Medical Research London, United Kingdom
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48
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Sayers Z, Aydin M, Bal E, Yesilirmak F, Konarev PV, Petoukhov MV, Roessle M, Kikhney AG, Shang W, Svergun DI. Comparative Characterization of Apo-, Reconstituted- and In Vivo-Folded forms of a Durum Wheat Metallothionein. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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49
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de Almeida Ribeiro E, Beich-Frandsen M, Konarev PV, Shang W, Večerek B, Kontaxis G, Hämmerle H, Peterlik H, Svergun DI, Bläsi U, Djinović-Carugo K. Structural flexibility of RNA as molecular basis for Hfq chaperone function. Nucleic Acids Res 2012; 40:8072-84. [PMID: 22718981 PMCID: PMC3439903 DOI: 10.1093/nar/gks510] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/05/2012] [Accepted: 05/09/2012] [Indexed: 12/22/2022] Open
Abstract
In enteric bacteria, many small regulatory RNAs (sRNAs) associate with the RNA chaperone host factor Q (Hfq) and often require the protein for regulation of target mRNAs. Previous studies suggested that the hexameric Escherichia coli Hfq (Hfq(Ec)) binds sRNAs on the proximal site, whereas the distal site has been implicated in Hfq-mRNA interactions. Employing a combination of small angle X-ray scattering, nuclear magnetic resonance and biochemical approaches, we report the structural analysis of a 1:1 complex of Hfq(Ec) with a 34-nt-long subsequence of a natural substrate sRNA, DsrA (DsrA(34)). This sRNA is involved in post-transcriptional regulation of the E. coli rpoS mRNA encoding the stationary phase sigma factor RpoS. The molecular envelopes of Hfq(Ec) in complex with DsrA(34) revealed an overall asymmetric shape of the complex in solution with the protein maintaining its doughnut-like structure, whereas the extended DsrA(34) is flexible and displays an ensemble of different spatial arrangements. These results are discussed in terms of a model, wherein the structural flexibility of RNA ligands bound to Hfq stochastically facilitates base pairing and provides the foundation for the RNA chaperone function inherent to Hfq.
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Affiliation(s)
- Euripedes de Almeida Ribeiro
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Mads Beich-Frandsen
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Petr V. Konarev
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Weifeng Shang
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Branislav Večerek
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Hermann Hämmerle
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Herwig Peterlik
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Dmitri I. Svergun
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Udo Bläsi
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
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50
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Filippov SK, Chytil P, Konarev PV, Dyakonova M, Papadakis C, Zhigunov A, Plestil J, Stepanek P, Etrych T, Ulbrich K, Svergun DI. Macromolecular HPMA-Based Nanoparticles with Cholesterol for Solid-Tumor Targeting: Detailed Study of the Inner Structure of a Highly Efficient Drug Delivery System. Biomacromolecules 2012; 13:2594-604. [DOI: 10.1021/bm3008555] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sergey K. Filippov
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, v. v. i., Heyrovský Sq. 2, 162 06 Prague
6, Czech Republic
| | - Petr Chytil
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, v. v. i., Heyrovský Sq. 2, 162 06 Prague
6, Czech Republic
| | - Petr V. Konarev
- European Molecular
Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Margarita Dyakonova
- Physik-Department, Technische Universität München, Physik-Department,
Fachgebiet
Physik weicher Materie, James-Franck-Str. 1, 85747 Garching, Germany
| | - ChristineM. Papadakis
- Physik-Department, Technische Universität München, Physik-Department,
Fachgebiet
Physik weicher Materie, James-Franck-Str. 1, 85747 Garching, Germany
| | - Alexander Zhigunov
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, v. v. i., Heyrovský Sq. 2, 162 06 Prague
6, Czech Republic
| | - Josef Plestil
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, v. v. i., Heyrovský Sq. 2, 162 06 Prague
6, Czech Republic
| | - Petr Stepanek
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, v. v. i., Heyrovský Sq. 2, 162 06 Prague
6, Czech Republic
| | - Tomas Etrych
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, v. v. i., Heyrovský Sq. 2, 162 06 Prague
6, Czech Republic
| | - Karel Ulbrich
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, v. v. i., Heyrovský Sq. 2, 162 06 Prague
6, Czech Republic
| | - Dmitri I. Svergun
- European Molecular
Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
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